Copper Quick Start Guide

Table of Contents

1. Introduction

This document provides a brief summary of information that you'll need to know to quickly get started working on Copper. For more detailed information, see the Copper User Guide.

2. Get a Kerberos Ticket

For security purposes, you must have a current Kerberos ticket on your computer before attempting to connect to Copper. A Kerberos client kit must be installed on your desktop to enable you to get a Kerberos ticket. Information about installing Kerberos clients on your Windows desktop can be found at HPC Centers: Kerberos & Authentication.

3. Connect to Copper

Copper can be accessed via Kerberized ssh as follows:

% ssh (# = 1 to 2)

4. Home and working

Each user has file space in the $HOME and $WORKDIR directories. The $HOME and $WORKDIR environment variables are predefined for you and point to the appropriate locations in the file systems. You are strongly encouraged to use these variables in your scripts.

NOTE: $WORKDIR is a "scratch" file system. The $WORKDIR file system is not backed up. You are responsible for managing files in your $WORKDIR directories by backing up files to the archive server and deleting unneeded files. Currently, $WORKDIR files that have not been accessed in 30 days are subject to being purged.

If it is determined as part of the normal purge cycle that files in your $WORKDIR directory must be deleted, you WILL NOT be notified prior to deletion. You are responsible to monitor your workspace to prevent data loss.

5. Transfer files and data to Copper

File transfers to DSRC systems must be performed using Kerberized versions of the following tools: scp, ftp, sftp, and mpscp. For example, the command below uses secure copy (scp) to copy a local file into a destination directory on a Copper login node.

% scp local_file (# = 1 to 2)

For additional information on file transfers to and from Copper, see the File Transfers section of the Copper User Guide.

6. Submit jobs to the batch queue

The Portable Batch System (PBS Professional ™) is the workload management system for Copper. To submit a batch job, use the following command:

qsub [ options ] my_job_script

where my_job_script is the name of the file containing your batch script. For more information on using PBS or on job scripts, see the Copper User Guide, the Copper PBS Guide, or the sample script examples found in the $SAMPLES_HOME directory on Copper.

7. Batch queues

The following table describes the PBS queues available on Copper:

Queue Descriptions and Limits on Copper
Priority Queue
Max Wall
Clock Time
Max Cores
Per Job
Highest urgent 168 Hours 4,096 Designated urgent jobs by DoD HPCMP
Down arrow for decreasing priority test 48 Hours N/A Staff-only testing
debug* 1 Hour 512 User testing
high 168 Hours 4,096 Designated high-priority jobs by Service/Agency
frontier 168 Hours 4,096 Frontier projects only
standard 168 Hours 4,096 Normal priority jobs
transfer 48 Hours 1 Data transfer for user jobs. Access to the long-term storage
Lowest background** 4 Hours 4,096 Unrestricted access - no allocation charge. Number of cores can be altered depending on the current system load.

* The running job limit on the debug queue per user is 4.
** The running job limit on the background queue per user is 6.

8. Monitoring your job

You can monitor your batch jobs on Copper using the qpeek, qview, or qstat commands.

The qstat command lists all jobs in the queue. The "-u username" option shows only jobs owned by the given user, as follows:

% qstat -u smith
                                                    Req'd  Req'd    Elap
Job ID   Username Queue    Jobname   SessID NDS TSK Memory Time  S  Time
-------- -------- -------- --------- ------ --- --- ------ ----- -  -----
1570853  smith    background tw2        --    1   1    --   12:00 R  01:12
1570854  smith    challenge  inspect    --    16  1    --   06:00 Q   --
1570939  smith    standard   45dh8      --     2  1    --   02:00 R  00:22

Notice that the output contains the JobID for each job. This ID can be used with the qpeek, qview, qstat, and qdel commands.

To delete a job, use the command "qdel jobID".

To view a partially completed output file, use the "qpeek jobID" command.

9. Saving your work

When your job is finished, you should archive any important data to prevent automatic deletion by the purge scripts.

Copy one or more files to the archive server
archive put [-C path ] [-D] [-s] file1 [file2 ...]

Copy one or more files from the archive server
archive get [-C path ] [-s] file1 [file2 ...]

For more information on archiving your files, see the Archive Guide.

10. Modules

Software modules are a very convenient way to set needed environment variables and include necessary directories in your path so that commands for particular applications can be found. Copper uses "modules" to initialize your environment with COTS application software, system commands and libraries, compiler suites, environment variables, and PBS batch system commands.

A number of modules are loaded automatically as soon as you log in. To see the modules that are currently loaded, run "module list". To see the entire list of available modules, run "module avail". You can modify the configuration of your environment by loading and unloading modules. For complete information on how to do this, see the Modules User Guide.

11. Available software

A list of software on Copper is available on the software page.

12. Advance Reservation Service

A subset of Copper's nodes has been set aside for use as part of the Advance Reservation Service (ARS). The ARS allows users to reserve a user-designated number of nodes for a specified number of hours starting at a specific date/time. This service enables users to execute interactive or other time-critical jobs within the batch system environment. The ARS is accessible via most modern web browsers at Authenticated access is required. Windows Internet Explorer users may authenticate with either CAC or YubiKey. Non-Windows users must use YubiKey. An ARS User's Guide is available online once you have logged in.